Similar regions between promoters of yaaO

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CTTTTAAAAACCAATACAATTGAAACTGCACGGGCAAATGAAAGAGGCCTTGTTGATATA hal ...........................................................A ste .TTGTGCAAACGAATAC...................AAGGAAAGAGG............. -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub GATACCTTGAAGAAGGTGCAGGAAAGCTTAATAAGCACGCTTGAAGAAACACTGACTATA hal GAAACACAGAAGGAGTAGCA....................TGGAAGAAACACAGA..... ste ...........................................................A -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> sub CAAGAAGAAGGACGAATCAAACGCCGTCAGGCAG-AAGAAGAGCTCATGATGATGGAAGG hal ............................................TCGTTATAATGGAAGA ste AACGAATACGGACGACCCGAAC...GACAGACAGCAAGGAAAGAGGATGATGATGGA... -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CGACCTGAAGCAAAAGCTGATTACAATAAAGGAAAGATGATTACCAGTAAGTCTGGCTTT hal AACACAGAAGGAGTAGC........AGATAGGAAAG--GATAACCAGAGAGT...GCCTT ste ............................AAGGAAAGAGGATGA................. -120 -110 -100 -90 -80 -70 sub AAGTTCTGTCAGAGGCACGATATAATAAGGTGTAAGAAGACACATTCAAAGGATTGTTTT hal ATGATCAGTCA....................................AAAGGTTTGTGTT ste ..GTTCTGGGACAGACAGCAAGGAAAGAGGATGATGATGGATCAAACGAA.......... -60 -50 -40 -30 -20 -10 sub C hal C ste . -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...